MolNFT v1 · #148105 · protein
Staphylococcus aureus superoxide dismutase soda
6EX3: “Staphylococcus aureus superoxide dismutase soda”. X-ray diffraction, 1 ligand (FE), 7 pockets (best druggability 0.58). MolNFT v1 #148105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EX3
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- W8TT57
- Ligands
- FE
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase (EC 1.15.1.1) | protein | 195 | 55% helix, 13% strand | W8TT57 |
| B | Superoxide dismutase (EC 1.15.1.1) | protein | 197 | 56% helix, 13% strand | W8TT57 |
| C | Superoxide dismutase (EC 1.15.1.1) | protein | 193 | 53% helix, 13% strand | W8TT57 |
| D | Superoxide dismutase (EC 1.15.1.1) | protein | 191 | 54% helix, 13% strand | W8TT57 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.58 | 0.82 | 23 | empty |
| 2 | 172 | 0.57 | 0.81 | 22 | empty |
| 3 | 189 | 0.56 | 0.80 | 23 | empty |
| 4 | 164 | 0.56 | 0.81 | 23 | empty |
| 5 | 109 | 0.38 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–C · 954 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 942 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6EX3 · Staphylococcus aureus superoxide dismutase SodA · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt W8TT57
- Elsewhere: RCSB PDB 6EX3 · PDBe 6EX3 · UniProt W8TT57
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